Coinfections of one host with multiple pathogen species are common, and have important implications for host health and pathogen fitness. In the research reported here, plant virus systems were used to explore the effects of coinfection on pathogen populations and host responses. Chapter 1 addresses the importance of coinfection timing using Barley yellow dwarf virus (BYDV-PAV) and Barley stripe mosaic virus. Coinfection timing significantly influenced viral within-host competition. Additionally, simultaneous coinfections were significantly more severe than sequential coinfections, which were only as severe as the most damaging constituent virus. A mathematical model was used to demonstrate that inaccurate projections of disease impacts on host populations can result when the effects of coinfection timing are not taken onto account. Chapter 2 explores the effects of coinfections of Cereal yellow dwarf virus (CYDV-RPV) and two species of BYDV (PAV and PAS) on pathogen evolution using an experimental evolution approach. Viruses exhibited altered within-host concentrations and transmission after serial passage in coinfections, without altered disease severity. Chapter 3 examines interactions between Bean common mosaic virus (BCMV) and Clover yellow vein virus (ClYVV)), and a microbial mutualist, rhizobia bacteria. The presence of rhizobia allowed ClYVV to reach higher within-host concentrations in coinfections. Viral transmission was also affected by interactions between coinfection and plant nitrogen source. Viral infection significantly reduced the percentage of nitrogen in plant tissues derived from microbial mutualists, with a greater than additive decrease in coinfections. Chapter 4 assesses the effects of BCMV and ClYVV coinfection and rhizobia colonization on plant primary and secondary metabolism. Increased photosynthetic rates were observed in plants colonized by rhizobia, which were driven by increased maximum rates of electron transport. Infection status, inorganic nitrogen fertilizer, and rhizobia had significant effects on components of plant volatile organic compound (VOC) emissions, with nitrogen source significantly affecting overall VOC profile composition. Chapter 5 analyzes how reductions in rhizobial nitrogen fixation caused by viral infection affect soil fertility, and projects substantial monetary losses for farmers when viral prevalence is high in a legume rotation, either due to additional fertilizer costs or reduced yield of a subsequent non-legume crop.